Well to make it short. I have encountered a bug with whats seems to be the elven alchemy labs. I have 6 running at once, I leave for say the night to let it build up. But it does not, depletes my gold and stone and the trickle for both endlessly keep going up without a single resource gain.
I have uploaded a short video of it. http://www.youtube.com/watch?v=DHA22X-MKVw
For now I just turn them off, relog and turn them back on and get what resources I can while I play and then turn them back off before I get off to do something else.

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"When the day gets long and contentious, I hold fast to my breath as a tiller and take each wave as it comes." - Patience

I have the same problem but i believe mine is related to wall construction I hope you guys put a fix in for that too. I have not played in like a week because i never have gold or stone unless i want to wait around while its gathered online and ofcourse turn off the wall construction that is constructing nothing. My wall have been done sense last month but every time i log in the auto wall construction is on again some how, and my gold and stone are at zero. I turned my Transmute towers off today well see if that changes something but they where to make gold so i dont see how it could change. sigh**** well i hope it gets fixed